Abstract: Background and Objective: Iodine excess is a risk factor in thyroid dysfunction. The purpose of the study was to identify the prolonged effect of iodine excess on thyroid dysfunction in areas with high iodine on natural resources in Indonesia. Materials and Methods: A cross-sectional study was conducted in two districts. This study included 500 School-Aged Children (SAC) 06-12 years of age for 25 clusters in each district, were included in this study. Logistic regression was performed to estimate the risk of thyroid dysfunction. Results: Demak and Grobogan were classified as iodine excess area with Median Urine Iodine Concentration (MUIC) is 446, 453 μg L–1, iodine water at 112.3, 414.5 ppb. Profile thyroid dysfunction was described as subclinical hypothyroidism, 31.5, 36.3%, secondary hypothyroidism, 25.5, 6.9%, respectively. While autoimmune thyroiditis was not shown, overt and subclinical hyperthyroidism was found in Grobogan only 0.4;1.4%. Excess iodine raises the risk of subclinical hypothyroidism, Adjusted Odd Ratio (AOR): 1.97 (CI:1.1-3.4) and secondary hypothyroidism, AOR: 2.44 (CI:1.5-3.9). Conclusion: Subclinical hypothyroidism is the most prevalent thyroid disease in iodine excess area due to elevated iodine in groundwater.